Grapevine

IGA has participated in the French-Italian Public Consortium for Grapevine Genome Characterizationthe first plant genome sequencing project conducted only by European research centres. At that time, the grapevine genome was the fourth one produced for flowering plants, the second for a woody species and the first for a fruit crop. IGA has contributed to the Sanger sequencing of a nearly-homozygous grapevine and to the genome assembly.

April 1, 2017

IGA has released an improved version of the genome assembly. This is the 12xV3 version of the PN40024 genome sequence from The French-Italian Public Consortium. Sequences of the scaffolds are unchanged compared to previous versions. We improved the chromosome assembly using new Hi-C data of chromatin interactions and high-density genetic maps.

The agp file describes order and orientation of scaffolds along chromosomes.

In the sequences of the chromosomes, 500 Ns were inserted between adjacent scaffolds. The multifasta file is downloadable at http://services.appliedgenomics.org/pub/grape-assembly/

Assembly summary

NAME: 12xV3; DATE OF RELEASE: 01-April-2017; GENOME CENTER: IGA

Scaffolds (> 2kb): 2,059 amounting to 485,185,630 bp

Scaffolds assigned to chromosomes: 1,125 amounting to 478,673,913 bp (coverage of the genome: 98.7 %)

Scaffolds ordered and oriented: 606 amounting to 473,438,004 bp (coverage of the genome: 97.6 %)

Unassigned scaffolds: 934 amounting to 6,511,717 bp (coverage of the genome: 1.3 %)

Length of the chromosomes

Telomeric repeats in chromosome sequences

MAJOR CHANGES OVER PREVIOUS VERSIONS:

All scaffolds included in the chromosome sequences are oriented.

Chromosome sequences in the 12xV3 version contain 35,7 Mb and 20,0 Mb that were unassigned (ChrUn) in the previous versions (12xV0 and 12xV2, respectively).

A substantial number of small scaffolds are assigned to three regions of residual heterozygosity on chromosomes 2, 7, and 10.

NOTES:

Scaffolds assigned to a chromosome, but not ordered or not oriented, are included in the chromosome_random sequence and are tagged “?” in the last column of the AGP.

ChrUn contains all the unplaced scaffolds, ordered according to decreasing size, and with unknown orientation.

Telomeric repeats were assembled in all chromosomes, except for the top of chromosomes 13 and 15 and the bottom of chr17.

 

Jaillon O et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463-467

Funded by the Italian Ministry of Agriculture (MIPAAF), additional funding from the Regional Government of Friuli Venezia Giulia (Italy)

Status: Vigna project, completed